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Detailed information for vg0615635376:

Variant ID: vg0615635376 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 15635376
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CAATAAATCAATTGGACGATGTCGAGAATCAGACTTATGTATGAATGGGCAAAGAACTCAGAATTCACATGACCAATTGGGCCAAAGTTCACAAGTCTGC[A/G]
TAGGAGAGCAACGGAGGAGGCCACCTGCCGATTTTGGGCCAGGCCGGCCCGACACATGGTTCGGCCGAACCCCCGCAGCGCCGTTCGATCCAGGTTTCTC

Reverse complement sequence

GAGAAACCTGGATCGAACGGCGCTGCGGGGGTTCGGCCGAACCATGTGTCGGGCCGGCCTGGCCCAAAATCGGCAGGTGGCCTCCTCCGTTGCTCTCCTA[T/C]
GCAGACTTGTGAACTTTGGCCCAATTGGTCATGTGAATTCTGAGTTCTTTGCCCATTCATACATAAGTCTGATTCTCGACATCGTCCAATTGATTTATTG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	36.20%	9.00%	5.16%	49.56%	NA
All Indica	2759	3.50%	11.70%	5.65%	79.09%	NA
All Japonica	1512	91.30%	1.00%	1.46%	6.22%	NA
Aus	269	69.90%	12.60%	4.83%	12.64%	NA
Indica I	595	3.50%	16.10%	4.20%	76.13%	NA
Indica II	465	2.60%	4.30%	3.66%	89.46%	NA
Indica III	913	1.80%	12.00%	8.54%	77.66%	NA
Indica Intermediate	786	6.10%	12.50%	4.58%	76.84%	NA
Temperate Japonica	767	96.50%	0.40%	0.26%	2.87%	NA
Tropical Japonica	504	83.10%	2.20%	3.17%	11.51%	NA
Japonica Intermediate	241	92.10%	0.40%	1.66%	5.81%	NA
VI/Aromatic	96	5.20%	46.90%	46.88%	1.04%	NA
Intermediate	90	46.70%	10.00%	8.89%	34.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0615635376	A -> G	LOC_Os06g27630.1	upstream_gene_variant ; 3557.0bp to feature; MODIFIER	silent_mutation	Average:13.254; most accessible tissue: Zhenshan97 root, score: 23.888	N	N	N	N
vg0615635376	A -> G	LOC_Os06g27630-LOC_Os06g27640	intergenic_region ; MODIFIER	silent_mutation	Average:13.254; most accessible tissue: Zhenshan97 root, score: 23.888	N	N	N	N
vg0615635376	A -> DEL	N	N	silent_mutation	Average:13.254; most accessible tissue: Zhenshan97 root, score: 23.888	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0615635376	1.25E-06	NA	mr1253_2	All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0615635376	1.03E-06	NA	mr1253_2	Ind_All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251